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Yorodumi- PDB-7fyd: Crystal Structure of human FABP5 in complex with 6-chloro-4-pheny... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fyd | ||||||
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Title | Crystal Structure of human FABP5 in complex with 6-chloro-4-phenyl-2-propan-2-ylquinoline-3-carboxylic acid | ||||||
Components | Fatty acid-binding protein 5 | ||||||
Keywords | LIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING | ||||||
Function / homology | Function and homology information regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Signaling by Retinoic Acid / long-chain fatty acid transmembrane transporter activity ...regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Signaling by Retinoic Acid / long-chain fatty acid transmembrane transporter activity / Triglyceride catabolism / epidermis development / fatty acid transport / long-chain fatty acid transport / secretory granule membrane / fatty acid binding / lipid metabolic process / glucose metabolic process / azurophil granule lumen / glucose homeostasis / positive regulation of cold-induced thermogenesis / postsynaptic density / synapse / lipid binding / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Ehler, A. / Benz, J. / Obst, U. / Ceccarelli-Simona, M. / Rudolph, M.G. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To be published Title: Crystal Structure of a human FABP5 complex Authors: Obst, U. / Magnone, C. / Kuhn, B. / Rudolph, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fyd.cif.gz | 44.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fyd.ent.gz | 29.8 KB | Display | PDB format |
PDBx/mmJSON format | 7fyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/7fyd ftp://data.pdbj.org/pub/pdb/validation_reports/fy/7fyd | HTTPS FTP |
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-Group deposition
ID | G_1002264 (222 entries) |
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Title | To be published |
Type | undefined |
Description | A set of fabp crystal structures |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15467.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FABP5 / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01469 | ||||||
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#2: Chemical | ChemComp-DMS / | ||||||
#3: Chemical | #4: Chemical | ChemComp-VLQ / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→47.61 Å / Num. obs: 26023 / % possible obs: 98.6 % / Redundancy: 12.569 % / Biso Wilson estimate: 26.949 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.069 / Χ2: 0.866 / Net I/σ(I): 20.41 / Num. measured all: 327093 / Scaling rejects: 4449 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: inhouse model Resolution: 1.45→47.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.687 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: clear ligand density, single close contact of isopropyl with cysteine note: ligand affinities in vitro may change depending on the degree of SS-bond formation
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.39 Å2 / Biso mean: 19.936 Å2 / Biso min: 10.75 Å2
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Refinement step | Cycle: final / Resolution: 1.45→47.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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